Impute a QFeatures object — impute

Impute the i assay in QFeatures object though impute function. The normalized assay is saved in the name assay.

Usage

impute_pe(
  pe,
  fun = c("QRILC", "bpca", "knn", "MLE", "MinDet", "MinProb", "man", "min", "zero",
    "mixed", "nbavg", "RF", "GSimp"),
  i = "peptideRaw",
  name = "peptideImp",
  ...
)

Arguments

pe: A QFeature object
fun: Character(1), imputation strategy, see impute.
i: A numeric or a character giving the index or the name, respectively, of the assay(s) to be processed.
name: Character(1), naming the new normalized assay. defaule is "peptideImp".
...: Other parameters to be passed to impute function.

Value

A QFeatures with a imputed assay in giving name.

Examples

if (FALSE) {
# Load example peptide data
data(Silicosis_peptide)
ecols <- grep("Intensity.", colnames(Silicosis_peptide), value = TRUE)

# Construct QFeature object
pe_peptides <- make_pe_parse(Silicosis_peptide, columns = ecols, remove_prefix = TRUE, log2transform = TRUE,mode = "delim")

# Filter, imputation
pe <- filter_pe(pe_peptides, thr = 1,fraction = 0.4, filter_formula = ~ Reverse != '+' & Potential.contaminant !="+" )
pe <- impute_pe(pe, fun = "QRILC")
}